Atomistic Simulations of Ion Channels - Computational Neuroscience: A Comprehensive Approach - page 54

Figure 2.8
A. Simulation model of OmpF porin in a dimyristoyl-phosphatidyl-choline bilayer.
The total system contains about 70,000 atoms. B. Close up of the eyelet region of
one of the OmpF monomers. There is a significant separation of positive charges
(blue) and negative charges (red) across the eyelet, resulting in a large local electric
field. (See color insert.)
molecules up to ca. 650 dalton. It shows gating behavior, but the molecular basis
and the physiological relevance of this phenomenon are not known [88]. OmpF is
weakly cation selective, and its selectivity depends on the ionic strength of the so-
lution. OmpF has been extensively studied by electrophysiology methods, although
not all of this data is straightforward to interpret in terms of the properties of a single
protein. Nonetheless, OmpF is an attractive model pore for calculations because its
high-resolution structure is known, as are structures of a range of mutants with al-
tered electrophysiological properties. This combination of high-resolution structures
and electrophysiological data allows systematic testing and calibrating of simulation
methods. Experimentally, OmpF is relatively easy to work with because it is present
in high concentrations in the outer membrane and it is very stable. Mutations are
also comparatively easy to make, which hopefully will facilitate testing of predic-
tions from simulations. Structurally, OmpF is a 16-stranded betabarrel, consisting of
three monomers. Porins have relatively long loops on the extracellular side and short
turns on the intracellular side. The L3 loops folds back into the pore and forms the
so-called eyelet region or constriction zone (Figure 2.8).